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comparison trinityrnaseq.xml @ 1:a34ce2b18877

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Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
author Jim Johnson <jj@umn.edu>
date Fri, 30 Aug 2013 10:56:26 -0500
parents d4ce07eb63bd
children 5eb99d21ef0d
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0:d4ce07eb63bd 1:a34ce2b18877
1 <tool id="trinityrnaseq" name="Trinity" version="0.0.1"> 1 <tool id="trinityrnaseq" name="Trinity" version="0.0.2">
2 <!-- Written by Jeremy Goecks, now maintained here by bhaas --> 2 <!-- Written by Jeremy Goecks, now maintained here by bhaas -->
3 <description>De novo assembly of RNA-Seq data Using Trinity</description> 3 <description>De novo assembly of RNA-Seq data Using Trinity</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2013-02-25">trinityrnaseq</requirement> 5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement>
7 <requirement type="package" version="1.0.0">bowtie</requirement>
6 </requirements> 8 </requirements>
7 <command> 9 <command>
8 Trinity.pl --JM $JM --CPU $CPU 10 Trinity.pl --JM $JM --CPU $CPU
9 11
10 ## Inputs. 12 ## Inputs.
39 #end if 41 #end if
40 #end if 42 #end if
41 43
42 44
43 ## direct to output 45 ## direct to output
44 > $trinity_log 2>&amp;1 46 | tee $trinity_log | grep 'Error'
45 47
46 </command> 48 </command>
47 <inputs> 49 <inputs>
48 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction"> 50 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
49 <option value="1G">1G</option> 51 <option value="1G">1G</option>
107 </when> 109 </when>
108 </conditional> 110 </conditional>
109 </inputs> 111 </inputs>
110 <stdio> 112 <stdio>
111 <exit_code range="1:" level="fatal" description="Faiiled" /> 113 <exit_code range="1:" level="fatal" description="Faiiled" />
114 <regex match="command not found"
115 source="both"
116 level="fatal"
117 description="Trinity.pl not found" />
118 <regex match="Error"
119 source="both"
120 level="fatal"
121 description="A trinity process failed" />
112 </stdio> 122 </stdio>
113 <outputs> 123 <outputs>
114 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> 124 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
115 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 125 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
116 </outputs> 126 </outputs>